An expert system to predict the forced degradation of organic molecules.

In this paper we describe Zeneth, a new expert computational system for the prediction of forced degradation pathways of organic compounds. Intermolecular reactions such as dimerization, reactions between the query compound and its degradants, as well as interactions with excipients can be predicted. The program employs a knowledge base of patterns and reasoning rules to suggest the most likely transformations under various environmental conditions relevant to the pharmaceutical industry. Building the knowledge base is facilitated by data sharing between the users.

Fine tuning reactivity: synthesis and isolation of 1,2,3,12b-tetrahydroimidazo[1,2-f]phenanthridines.

A facile route for the synthesis and isolation of 1,2,3,12b-tetrahydroimidazo[1,2-f]phenanthridines (TIPs) has been developed. The heterocycle is a reactive intermediate in the three-step cascade synthesis of 2,3-dihydro-1H-imidazo[1,2-f]phenanthridinium cations (DIPs), a biologically active DNA intercalating framework; however, the intermediate has previously only been characterized in situ. Derivatization of the structure at the imidazo-N position controls the reactivity of the intermediate with respect to electronic potential and pK(a) allowing isolation of a selection of TIP structures. Correlations between these parameters and reaction outcome have been made, and other influences such as steric and solvent effects have also been investigated.

A new C-C bond forming annulation reaction leading to pH switchable heterocycles.

A C-C bond forming reaction resulting from the alpha-addition of carbon based nucleophiles to N-bromoethyl phenanthridinium leads to the formation of 2,3-dihydro-12H-pyrrolo[1,2-f]phenanthridine-based derivatives which undergo reversible ring-opening/closing under pH control.

Spontaneous assembly and real-time growth of micrometre-scale tubular structures from polyoxometalate-based inorganic solids.

We report the spontaneous and rapid growth of micrometre-scale tubes from crystals of a metal oxide-based inorganic solid when they are immersed in an aqueous solution containing a low concentration of an organic cation. A membrane immediately forms around the crystal, and this membrane then forms micrometre-scale tubes that grow with vast aspect ratios at controllable rates along the surface on which the crystal is placed. The tubes are composed of an amorphous mixture of polyoxometalate-based anions and organic cations. It is possible for liquid to flow through the tubes, and for the direction of growth and the overall tube diameter to be controlled. We demonstrate that tube growth is driven by osmotic pressure within the membrane sack around the crystal, which ruptures to release the pressure. These robust, self-growing, micrometre-scale tubes offer opportunities in many areas, including the growth of microfluidic devices and the self-assembly of metal oxide-based semipermeable membranes for diverse applications.

Realization of a "lockable" molecular switch via pH- and redox-modulated cyclization.

A switchable organic system involving four distinct states that can be interconverted by use of both pH and redox chemistry as control parameters has been developed. The key molecules involved in this system are the phenanthridine-based heterocycles 1-isobutyl-1,2,3,12b-tetrahydroimidazo[1,2-f]phenanthridine (TIP) and 5-[2-(isobutylamino)ethyl]phenanthridinium (AEP). These two states are interchangeable via pH control, and in addition they can also be further manipulated by oxidation or reduction to convert them to their "pH-inert" forms: 1-isobutyl-2,3-dihydro-1H-imidazo[1,2-f]phenanthridinium (DIP) and 5-[2-(isobutylamino)ethyl]-5,6-dihydrophenanthridine (AEDP), respectively. UV and (1)H NMR experiments carried out in a biphasic dichloromethane (DCM)/water solution were used for in situ structure determination. The results showed that the pH-modulated cyclization and phase-transfer process between the TIP and AEP states was essentially quantitative and repeatable without any significant loss in activity and that reduction or oxidation could be used to lock out these states against such acid-base-induced changes.

Metal-mediated transformation of a triazinephenanthridinium ligand leading to a {Pd5} coordination complex observed crystallographically and by cryospray mass spectrometry.

The formation of a pentanuclear palladium(II) complex with a phenanthridinonetriazine-based ligand system, which itself is formed by a metal-mediated rearrangement of a triazinephenanthridinium proligand, is described.

Incorporation of N-heterocyclic cations into proteins with a highly directed chemical modification.

N-Heterocyclic cations are incorporated into proteins using 5-(2-bromoethyl)phenanthridinium bromide, which selectively reacts with either cysteine or lysine residues, resulting in ethylphenanthridinium (Phen) or highly stable cyclised dihydro-imidazo-phenanthridinium (DIP) adducts respectively; these modifications have been found to manipulate the observed structure of lysozyme and bovine serum albumin by AFM.

A general and efficient five-step one-pot procedure leading to nitrogen-bridgehead heterocycles containing an imidazole ring.

A very simple annulation reaction was designed, allowing an imidazole moiety to be fused onto a range of pyridine-based derivatives. The methodology consists of an activation step via the formation of a pyridinium salt to increase the electrophilicity of the pyridine ring, followed by a cascade reaction triggered by a nucleophilic attack of the iminium moiety. Depending on the pyridinium salt, it is possible to obtain functionalized imidazole moieties.

Microcalorimetry of interaction of dihydro-imidazo-phenanthridinium (DIP)-based compounds with duplex DNA.

Isothermal titration (ITC) and differential scanning calorimetry (DSC) have been used to screen the binding thermodynamics of a family of DNA intercalators based on the dihydro-imidazo-phenanthridinium (DIP) framework. All members of this DIP-based ligand family bind to both genomic (calf thymus and/or salmon testes) and a synthetic dodecamer d(CGCGAATTCGCG) duplex DNA with broadly similar affinities regardless of side chain size or functionality. Viscosity measurements confirm that binding satisfies standard criteria for intercalation. Binding is exothermic but with an additional favourable positive entropy contribution in most cases at 25 degrees C, although a significant negative heat capacity effect (DeltaC(p)) means that both DeltaH(0) and DeltaS(0) decrease with increasing temperature. DIP-ligand binding to DNA also shows significant entropy-enthalpy compensation effects that are now almost standard in such situations, probably reflecting the conformational flexibility of macromolecular systems involving a multiplicity of weak non-covalent interactions. This ability to vary side chain functionality without compromising DNA binding suggests that the DIP framework should be a promising basis for more adventurous chemistry at the DNA level.

Dihydroimidazophenanthridinium (DIP)-based DNA binding agents with tuneable structures and biological activity.

We have synthesised a library of dihydroimidazophenanthridinium cations (DIPs) with large structural diversity (1-29) using a "one-pot" approach. The DNA binding constants of DIPs range from 2x10(4) to 1.3x10(5) M(-1), and the free energies for binding range from -5.9 to -6.40 kcal mol(-1). Viscosity measurements demonstrated that the binding of the compounds caused DNA lengthening, thus signifying binding by intercalation. The cytotoxicities of the compounds were determined by tetrazolium dye-based microtitration assays and showed a large range of values (0.09-11.7 microM). Preliminary molecular modelling studies of the DNA-DIP interactions suggested that the DIP moieties can interact with DNA by intercalation, and some R groups might facilitate binding by minor-groove binding. The results provide insight into how to design biologically active DNA binding agents that can interact in these ways.

Discovery of an imidazo-phenanthridine synthon produced in a 'five-step one-pot reaction' leading to a new family of heterocycles with novel physical properties.

A new class of heterocyclic aromatic cation with novel physical properties has been constructed by an unprecedented reaction pathway that proceeds via five spontaneous steps to yield a 'synthon' that can be further derivatised by a final nucleophilic substitution step.

Highly stable phenanthridinium frameworks as a new class of tunable DNA binding agents with cytotoxic properties.

A new class of cytotoxic heteroaromatic cations is presented, based on the dihydro-imidazo-phenanthridinium framework (DIP), that have affinity for DNA and cytotoxicity toward cancerous cells. The DIP framework is particularly tunable due to the flexible synthetic methodology. Furthermore, the central moiety has proved to be very stable to hydrolysis and reduction compared to other phenanthridinium-based agents.

General one-pot, three-step methodology leading to an extended class of N-heterocyclic cations: spontaneous nucleophilic addition, cyclization, and hydride loss.

A new class of phenanthridinium derivative has been isolated from the reaction of 2-bromoethyl-phenanthridinium bromide with a range of primary amines in excellent yields. The reaction pathway is unprecedented and proceeds via three cascade steps: nucleophilic attack of a primary amine on the iminium moiety of a heteroaromatic ring system and cyclization to form a five-membered ring, followed by hydride loss to yield a rearomatized dihydro-1H-imidazo[1,2-f]phenanthridinium derivative. A range of NMR phase transfer experiments were carried out to elucidate the mechanistic pathway, and the methodology has been further developed by means of a biphasic system using N-bromosuccinimide as a co-oxidizing agent. The method has also been extended to other N-heterocyclic cation derivatives such as quinolinium and quinazolinium.